Transcription factor binding to enhancer elements is critical for proper gene regulation. Enhancers are often found in noncoding sequences in close proximity to the gene that they regulate and sometimes even on another chromosome; however, whether they are also found in exons, the coding regions of DNA, is unclear. Birnbaum et al. analyzed 25 mouse and human enhancer-associated ChIP-seq data sets in order to identify enhancer peaks that overlap exons and found regulatory transcription factor binding to exonic regions. In fact, in mice, roughly 7% of enhancer peaks overlapped coding exons. Mutation of these elements in zebrafish and mouse enhancer assays showed that although exonic sequences are necessary, they are not sufficient for full enhancer function. Absence of an exon-encoded enhancer, however, did have functional consequences. Thus, exonic sequences may function in the regulation of nearby genes. Moreover, phenotypes seen in genetic knockout animals may be the result of not only the lack of expression of the deleted gene but also alterations in the expression of genes that are regulated by enhancers in the deleted exons.